Browsing by Subject "High-throughput"
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Item Open Access A High-Throughput Framework for Materials Research And Space Group Determination Algorithm(2012) Taylor, Richard HansenEffective computational materials search, categorization, and design necessitates a high-throughput (HT) approach. System by system analyses lack the scope and speed needed to uncover large portions of the materials landscape. By performing broad searches over structural or chemical classes of materials and guided by fundamental physical principles, materials with specific desired properties can be systematically found. Furthermore, the HT approach is an effective general tool for materials classification. Depending on the application, various properties can be computed leading to powerful classification schemes. To implement HT materials studies, however, a versatile and robust framework must first be developed. In this paper, the HT framework AFLOW that has been developed and used successfully over the last decade is presented. Specifically, attention is given to an origin-specific symmetry algorithm. The algorithm is designed to determine the relevant symmetry properties of an arbitrary crystal structure (e.g., point group, space group, etc.).
Item Open Access Autonomous Symmetry Analysis and Structure Prototyping for Materials Discovery(2019) Hicks, David JonathanThe structure-property relationship is the foundation for materials modeling, predicting the behavior of compounds based on structural characteristics. With the advancement of ab initio methods and high performance computing, atomic configurations are being explored at an unprecedented rate. To effectively navigate the vast search space, procedures are presented for analyzing and prototyping crystalline compounds for high-throughput simulation. Integrated into the Automatic Flow (AFLOW) framework for computational materials discovery, these tools are the underlying workhorse for symmetry classification and materials generation. In particular, algorithms are detailed for determining the set of isometries for crystals, featuring a comprehensive collection of symmetry descriptions along with routines to handle ill-conditioned structural data. A library of crystallographic structures is also introduced — showcasing nearly 600 prototypes with representatives from each space group — and is complemented with functionality for rapidly creating materials via prototype decoration. Lastly, a module for comparing crystalline compounds is described to identify duplicate entries within large data sets and detect novel structure-types, independent of representation. Mechanisms are featured for converting geometries into a standard prototype convention, providing a direct pathway for incorporation into the crystallographic library. With these autonomous computational approaches, compounds are automatically classified and generated, enabling the design of new and structurally distinct materials.
Item Open Access Chromatin Determinants of the Eukaryotic DNA Replication Program(2011) Eaton, Matthew LucasThe accurate and timely replication of eukaryotic DNA during S-phase is of critical importance for the cell and for the inheritance of genetic information. Missteps in the replication program can activate cell cycle checkpoints or, worse, trigger the genomic instability and aneuploidy associated with diseases such as cancer. Eukaryotic DNA replication initiates asynchronously from hundreds to tens of thousands of replication origins spread across the genome. The origins are acted upon independently, but patterns emerge in the form of large-scale replication timing domains. Each of these origins must be localized, and the activation time determined by a system of signals that, though they have yet to be fully understood, are not dependent on the primary DNA sequence. This regulation of DNA replication has been shown to be extremely plastic, changing to fit the needs of cells in development or effected by replication stress.
We have investigated the role of chromatin in specifying the eukaryotic DNA replication program. Chromatin elements, including histone variants, histone modifications and nucleosome positioning, are an attractive candidate for DNA replication control, as they are not specified fully by sequence, and they can be modified to fit the unique needs of a cell without altering the DNA template. The origin recognition complex (ORC) specifies replication origin location by binding the DNA of origins. The S. cerevisiae ORC recognizes the ARS (autonomously replicating sequence) consensus sequence (ACS), but only a subset of potential genomic sites are bound, suggesting other chromosomal features influence ORC binding. Using high-throughput sequencing to map ORC binding and nucleosome positioning, we show that yeast origins are characterized by an asymmetric pattern of positioned nucleosomes flanking the ACS. The origin sequences are sufficient to maintain a nucleosome-free origin; however, ORC is required for the precise positioning of nucleosomes flanking the origin. These findings identify local nucleosomes as an important determinant for origin selection and function. Next, we describe the D. melanogaster replication program in the context of the chromatin and transcription landscape for multiple cell lines using data generated by the modENCODE consortium. We find that while the cell lines exhibit similar replication programs, there are numerous cell line-specific differences that correlate with changes in the chromatin architecture. We identify chromatin features that are associated with replication timing, early origin usage, and ORC binding. Primary sequence, activating chromatin marks, and DNA-binding proteins (including chromatin remodelers) contribute in an additive manner to specify ORC-binding sites. We also generate accurate and predictive models from the chromatin data to describe origin usage and strength between cell lines. Multiple activating chromatin modifications contribute to the function and relative strength of replication origins, suggesting that the chromatin environment does not regulate origins of replication as a simple binary switch, but rather acts as a tunable rheostat to regulate replication initiation events.
Taken together our data and analyses imply that the chromatin contains sufficient information to direct the DNA replication program.
Item Open Access Computational Materials Genome Initiative by High-Throughput Approaches(2013) Xue, JunkaiRecently, in materials innovations, computational methods are used more frequently than in past decades. In this thesis, the materials genome initiative, an advanced new framework, will be introduced. With this blueprint, our efficient high-throughput software, AFLOW, has been implemented with several compatible functions for ma- terials properties investigations, such as prototype searching, phase diagram studying and magnetic properties discovering. With this effective tool, we apply ab initio cal- culations to discover new generation of specific materials properties.
An efficient algorithm for prototypes comparision has been designed and imple- mented into our high-throughput framework AFLOW. In addition, prototypes clas- sification was utilized to differentiate the our materials database. This classification will accelerate the materials properties searching speed. With respect to structure prototypes, low temperature phase diagrams were used for binary and ternary alloy systems stability investigation. The alogrithms have been integrated into AFLOW. With this tool, we systematically explored the binary Ru systems and Tc systems and predicted new stable compounds.